This tutorial paper focuses on the design, simulation, and optimization of polymerase–exonuclease–nickase (PEN) toolbox systems. The PEN toolbox is a molecular programming framework that relies on the interaction between DNA molecules and enzymes to produce highly non-linear dynamic systems. The flip side of that expressivity is that the design of systems relies heavily on trial-and-error, thus calling for computer assistance. The paper includes a description of the high-level application programming interface of DACCAD, the main simulation library for PEN toolbox systems, and introduces methods to extend the existing software to match the designer’s needs. Several examples are provided to illustrate that approach.

中文翻译：

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使用 PEN 工具箱设计动态分子系统

本教程论文侧重于聚合酶-外切核酸酶-切口酶 (PEN) 工具箱系统的设计、模拟和优化。PEN 工具箱是一个分子编程框架，它依赖于 DNA 分子和酶之间的相互作用来产生高度非线性的动态系统。这种表现力的另一面是系统设计在很大程度上依赖于反复试验，因此需要计算机辅助。本文包括对 PEN 工具箱系统主要仿真库 DACCAD 的高级应用程序编程接口的描述，并介绍了扩展现有软件以满足设计者需求的方法。提供了几个示例来说明该方法。